ThermoFisher.CommonCore.XcaliburQuantitation

Calibration and QuantificationResult flags based on various threshold values

Initializes a new instance of the class. Default constructor

Initializes a new instance of the class. Copy constructor

interface to copy from

Gets or sets a value indicating whether the sample is above the LOD.

true if [detection passed]; otherwise, false.

Gets or sets a value indicating whether the sample is below the Rsquared limit.

true if [R square passed]; otherwise, false.

Gets or sets a value indicating whether the sample is below the limit of quantitation.

Gets or sets a value indicating whether the sample is below the linearity limit.

Gets or sets a value indicating whether the sample is above the carry over limit. This is usually displayed only for blanks.

Creates a new object that is a copy of the current instance.

A new object that is a copy of this instance.

Calibration and QuantificationResult threshold values. This set of flags is based on backwards compatibilty with the products "Xcalibur" and "LCquan". See also "FlaggingThresholds" for an alternative (larger) set of thresholds.

Initializes a new instance of the class. Default Constructor

Initializes a new instance of the class. Construct instance from interface, by cloning all settings

Interface to clone

Gets or sets the carry over limit threshold.

The carry over limit threshold.

Gets or sets the detection limit threshold.

The detection limit threshold.

Gets or sets the linearity limit threshold.

The linearity limit threshold.

Gets or sets the quantitation limit threshold.

The quantitation limit threshold.

Gets or sets the R squared threshold.

The R squared threshold.

Gets or sets the limit of reporting. A value should only be reported if it is >= the limit of reporting. This value is used to calculate the ReportingLimitPassed flag.

Creates a new object that is a copy of the current instance.

A new object that is a copy of this instance.

Gets the Calibration and Quantification flags. Call this from within ComponentIntegrationResults.CalculateAmounts under the comment: "set flags". Set the CalculatedAmount from m_results.CalculatedAmount and RSquaredResults from componentCalibration.RSquared.

The calculated amount. The R squared results. The dilution factor. The .

Class to perform flagging tests on calibration standards

Gets or sets limits on calculated amount

Evaluate flags on calibration standards

Calibration curve R Squared value Amount calcualated (concentration) of the compound. Base amount for cal level Access to percent RSD and percent CV The .

Convert a true/false result to "Pass", "fail".

Value of threshold for this test. If the threshold is zero, the the result is always "not tested". Else: The true/false result converts to pass/fail The .

Results of Tests which should be done on any calibration sample type

Initializes a new instance of the class. Default constructor

Initializes a new instance of the class. Make a copy of object

object to copy

Gets or sets the results of testing the curve "RSquared" value against the minimum. Must be above minimum for this to pass

Gets or sets the results of testing the curve "RSquared" value against the maximum. Must be below maximum for this to pass

Gets or sets results of testing that the percent difference from the known base amount of a standard from the measured value on the calibration curve is within limits (+/-).

Gets or sets results of testing that the CV of the standard is below the limit

Creates a new object that is a copy of the current instance.

A new object that is a copy of this instance. 2

Holds the data associated with the Internal Standard setup from the calibration page.

Gets or sets the amount of internal standard. Not used in any calculation yet.

Gets or sets the units for the internal standard

Initializes a new instance of the class. Default Constructor

Initializes a new instance of the class. Construct instance from interface, by cloning all settings

Interface to clone

Creates a new object that is a copy of the current instance.

A new object that is a copy of this instance.

Updates the data items in this class.

The amount. The units.

Holds all the information to be shown and relating to calibration setup parameters.

Gets or sets the target compound settings.

The target compound settings.

Gets or sets the internal standard settings.

The internal standard settings.

Gets or sets the component type, which determines if this component is a target compound or an internal standard

Gets the target compound settings.

The target compound settings.

Gets the internal standard settings.

The internal standard settings.

Initializes a new instance of the class. Default constructor

Initializes a new instance of the class. Construct instance from interface, by cloning all settings

Interface to clone

Creates a new object that is a copy of the current instance.

A new object that is a copy of this instance.

Updates the the settings between internal and external standard

Change the method to internal or external mode

Holds the data associated with the Target Compound setup from the calibration page.

Gets or sets the table of calibration levels

Gets or sets the table of QC levels

Gets or sets the calibration curve fitting method

Gets or sets the weighting for calibration curve

Gets or sets the calibration curve origin mode

Gets or sets a value which determines how the response should be measured (using either peak height or peak area).

Gets or sets the units (of concentration) of the calibration compound. For example "mg/ml"

Gets or sets the name of the internal standard for this component

Gets or sets the isotopic contribution of the internal standard to the target compound

Gets or sets the isotopic contribution of the target compound to the internal standard

Gets the table of calibration levels

Gets the table of QC levels

Initializes a new instance of the class. Default constructor

Initializes a new instance of the class. Construct instance from interface, by cloning all settings

Interface to clone

Find a quality control level.

The level name. The or null of not found.

Changes between internal and external standard

This is set if the method was previously internal standard, and has been updated by the user to be external standard. If this is true, then all calibration levels are reset.

Creates a new object that is a copy of the current instance.

A new object that is a copy of this instance.

Limits for flag testing on calibration samples

Initializes a new instance of the class. Create a copy of this object from an interface

Object to copy from

Initializes a new instance of the class. Default constructor

Initializes a new instance of the class.

The thresholds. Thrown when thresholds are null

Gets or sets the Maximum acceptable relative standard deviation for a given compound.

Gets or sets the Minimum acceptable value of R Squared

Gets or sets the Maximum percent difference between actual and predicted amount

Gets or sets the Maximum value of Percent CV

Creates a new object that is a copy of the current instance.

A new object that is a copy of this instance. 2

Quantitation values calculated for a component.

Gets or sets the peak for use with manual mode

Gets the peak for use with manual mode

Gets or sets a value indicating whether the detected peak is manually created. When manual mode is true, requesting "Peak" gets the manual peak

Gets the results of component detection. The detected peak plus additional data.

Gets the current peak for this results When the result is in manual mode, this is the manual peak When the result is not manual (automatic) then this is peak information from to automatic located peak

Gets or sets the results of component detection. The detected peak plus additional data.

Gets a value indicating whether a peak has been found. Always true for manual peaks.

Gets a value indicating whether RT adjustments could be made to the RT reference. This flag is only meaningful when RT reference adjustments are made based on a reference peak (see the locate class). If a valid reference peak is supplied, then the expected RT can be adjusted based on the reference. If no reference peak is found (a null peak) then the expected RT cannot be adjusted, and this flag will be false.

Gets or sets the name of the component which created these results

Gets or sets The scan at peak apex

The segmented scan object.

Gets or sets a value indicating whether this is a centroid scan. If true: display as sticks (centroid data) else display as connected lines (profile data)

Gets or sets the scan stats.

The scan stats.

Gets or sets the chromatogram trace for this peak

Gets or sets data such as serial number for the instrument used to read the chromatograms. This can be null when there is no valid data. (no signal read yet).

Gets data such as serial number for the instrument used to read the chromatograms. This can be null when there is no valid data. (no signal read yet).

Gets or sets the ratio of height to internal standard height

Gets or sets the ratio of area to internal standard area

Gets or sets a value which determines how ratios are reported, either by height or area. This is initialized from the component in "FromComponent"

Gets or sets the internal standard area

Gets or sets the internal standard height

Gets or sets the amount calculated for this component

Gets or sets information about the peak relative to the calibration curve, such as "Response High"

Gets or sets the results of system suitability checks

Gets the results of system suitability checks

Gets the results of all IRC calculations for this component

Gets or sets a value indicating whether all IRC tests have passed, or IRC is never run.

Gets or sets the calibration and quantification flags.

The calibration and quantification flags.

Gets the calibration and quantification flags.

The calibration and quantification flags.

Gets or sets the detection threshold flags.

The detection threshold flags.

Gets the detection threshold flags.

The detection threshold flags.

Gets the ion ratio signals.

The ion ratio signals.

Gets the ion ratio signals.

The ion ratio signals.

Gets the value to use for the calibration curve. Either the area ratio or height ratio (depending on calibration settings)

Gets either the area or height (depending on calibration settings)

Gets the area of the peak

Gets the height of the peak

Initializes a new instance of the class. Default constructor (empty results)

The initialize.

Duplicate the results

object to copy in to

Creates a new object that is a copy of the current instance.

A new object that is a copy of this instance. 2

Initializes a new instance of the class. Construct this from another object

Object to copy from

Initializes a new instance of the class. Construct this from another object

Object to copy from If true, all items from raw files (scans, chromatograms, IRC chromatograms, scan stats) found in the component results are copied. If false, these are all set to new objects. Applications should then read these items as needed from "file integration results" or from the raw file

Initialize from component results.

Access to the component results. True if this class should keep a copy of raw data.

Prepares the segmented scan from the raw file. The scan is read based on the retention time of the peak apex. Assumes that the caller has already selected the required data stream from the file

The raw file.

Calculates the area and height ratios, based on an internal standard

The internal standard

Calculates the area and height ratios, based on an internal standard

True if this component has an internal standard The internal standard peak Percentage of internal standard in target compound Percentage of target compound in internal standard

Manually integrate this component, from the signal previously created. Also sets so that the new manual peak is returned by the Peak method.

Start time of baseline Start intensity of baseline end time of baseline end intensity of baseline

Gets either the or depending on the methodCalibrationSettings. TargetCompoundSettings.Response.

The method calibration settings. The response for this component

Copy a manually integrated peak from previous results

previously integrated results

The set peak flags.

The calibration limits. The detection threshold limits. The check based on calculated amount. The table. The component calibration. The dilution factor. The quality control level.

Calculate flags for each sample type

Information about sample (for example cal or qc level) settings for component R Squared of regression Calibration curve replicates

Gets or sets the results of flag calculations per sample type

Gets FlaggingResults.

Mock implementation of IReplicateStatisticsAccess, to return 0 for all values

Gets PercentRSD.

Gets PercentCV.

Gets AverageRetentionTime.

Gets AverageRf.

Gets a value indicating whether the results are Valid.

The check response.

The calculated. The lowest. The highest. The origin mode.

The check response.

The check based on calculated amount. The table.

Calculate the amount for this component, and then calculate the peak flags

Settings for component (needed for flagging) Calibrated data for this component. Dilution of the sample, used in threshold calculations. Level used to set peak flags

Calculate the amount for this component.

Calibrated data for this component.

Calculate the peak flags for this component.

Calibrated data for this component. Settings for component (needed for flagging) Dilution of the sample, used in threshold calculations. Level used to set peak flags

Gets or sets the name of the raw file which was used to create this data

All replicates of all calibration levels for one component

Internally used string to keep statistics about the internal standards, in the replicate tables.

Initializes a new instance of the class. Default constructor (to serialize) Application should rely on to initialize this table

Initializes a new instance of the class. Copy constructor Create (deep) copy of the replicate table.

The replicate Table.

Initializes a new instance of the class.

The calibration settings. component name

Gets the settings used to create this table

Gets or sets the name of component which made this replicate table

Gets or sets Coefficients for the fitted calibration curve. This has a setter for serialization only.

Gets the amount of the highest calibration level (high limit of calibration)

Gets the highest response included on the calibration curve. This is only valid after the curve has been created.

Gets the calibration standards at each level for this component, from previous sequences. Data to create the calibration curve. This data is not changed by "batch processing" of a sequence. It is merged with any calibration data from the current sequence to create the set of points used for the calibration curve.

Gets the amount of the lowest calibration level (low limit of calibration)

Gets the lowest response included on the calibration curve. This is only valid after the curve has been created.

Gets the replicates of quality control levels, used to calculate statistics on QCs

Gets an interface to calculate amounts for this component, based on the calibration results.

Gets the calibration standards at each level for this component. Data to create the calibration curve.

Gets the settings used to create this table

Gets or sets a value indicating whether the table is being used for replicates of an internal standard.

Create a ComponentReplicateTable from Calibration Settings

The component's calibration settings The component's name The replicate table

Create a replicate table from the calibration levels

The calibration levels A new replicate table, with the correct calibration levels for the given component.

Finds the replicate with amount and response from the the current sequence or the historic sequence replicates table. The current sequence data is searched first.

The amount. The response. null if not found.

Finds the replicate with amount and response from the historic sequence replicates table.

The amount. The response. null if not found.

Finds the item with the name that matches the level, in the historic replicates table.

The level. Interface to access the requeste replicates.

Finds the item with the name that matches the level.

The level to find Interface to read the requested replicates.

Finds the replicate with amount and response from the current sequence replicates table.

The amount. The response. null if not found.

Finds the item with the name that matches the level.

The level. Interface to read the requested replicates.

Apply all "include exclude" conditions from replicates to the current table. This may be needed if a replicate table is rebuild (after manual integration etc.)

Table who's exclusions are copied.

Create the historic replicates for this table, based on a previous replicate table

The table to be attached.

Creates a new object that is a copy of the current instance. This is a shallow clone.

A new object that is a copy of this instance. 2

Generate tables of data for the calibration curve, based on the replicate table

A data table, which can be used to plot a calibration curve.

Create a calibration curve based on the supplied settings and replicates

Finds the replicate with amount and response from the current sequence or the historic sequence replicates table. The current sequence data is searched first.

The amount. The response. null if not found.

Finds the replicate with amount and response from the historic sequence replicates table.

The amount. The response. null if not found.

Finds the item with the name that matches the level, in the historic replicates table.

The level. The table that was found, or null if no such level.

Finds the replicate with amount and response from the current sequence replicates table.

The amount. The response. null if not found.

Finds the item with the name that matches the level.

The level to find The table that was found, or null if no such level.

Finds the replicate with amount and response from the current sequence replicates table.

The amount. The response. null if not found.

Finds the item with the name that matches the level.

The level. The table that was found, or null if no such level.

The merge replicates.

The all replicates. The external replicates.

calculate response bounds (lowest and highest response).

The replicates (with stats).

Calculate the RSD and percent CV (coefficient of variance) for all levels

The replicates With stats. The percent RSD Calculator.

Overall calibration method.

Calibrate using internal standard

Calibrate using external standard.

RSD Calculation

Use calculated amount

Use response values

Determines how the peak's response relates to the calibration curve

Nothing unusual (point within curve)

The response was above the calibration curve (extrapolated above)

The response was below the calibration curve (extrapolated below)

QC tests were outside of limits

Reference Mode set of possibilities

Use Expected Time (default)

Adjust Using a Reference compound

Use this compound As a Reference for another compound

Use As Void Time (1st peak to judge others from.)

Specific results of AddComponent, RenameComponent, and DeleteComponent methods. This results makes it easier for caller to validate return and decide what to do.

Successfully completed operation

Selected name was not found (in all methods).

New name to add or rename to is found in list. Cannot do that.

User entered an empty string. That is disallowed.

Determines what criteria is used to evaluate a matrix blank sample

Evaluate based on percentage of Limit Of Reporting (from "Quantitation" thresholds)

Evaluate based on percentage of Limit Of Detection (from "Quantitation" thresholds)

Evaluate based on percentage of LimitOfQuantitation (from "Quantitation" thresholds)

Evaluate based on percentage of Maximum Concentration.

Wrapper for fast access to the list of components.

The object which is being wrapped (apart from the component finding)

Fast lookup table for a component

The from method.

The method. The .

Wrap the method.

The method.

Find a component in the method by name

The name to search for The found component, or null if no match

Gets the set of components (target compounds and standards) in the method

Gets the mass options.

The mass options.

Gets the processing options object. Don't need a setter function, always refer to the options from this method.

The processing options.

Method to give progress for a list of named items. Called twice per item. Implementor should return false to continue processing, or true to cancel.

The item being processed (for example, component name, sample name, depending on context) This is true on the first call, before any work is done on this item and false on the second call (after this item is processed) The number of items which have been completed. Incremented between the "before" and "after" calls for each item The total number of items which will be processed True if processing should be canceled

Results of integration for all components in 1 file. This class manages the integration of a single file. It can generate results for all components in a file, which can then be serialized.

Gets or sets the sample information for this raw file

Gets the results for each component

Gets or sets the results per component. For serialization support. Apps should use "Results"

Gets or sets the zero based index into the sequence for this row

Gets or sets summary information about the raw file

Gets the sample information for this raw file

Perform integration on all components in one file. Integration of a file involves generating chromatograms for each component, performing checks such as Ion ratio and System suitability on the peaks and calculating the relative responses to internal standards. Retention time reference components are integrated first, then others based on the adjusted times.

Zero based index into the sequence for this row Row of the sequence (sample information) Processing method Is set, signals created (chromatograms) during peak detection are maintained. This can be used later for manual integration, or chromatogram displays. However, since chromatogram signals consume large amounts of memory, set this to false if you will not need to access them later Tool to supply data stream based on file name The results for this file.

Finds the results for component.

The name of the component to find. The results for the named component, or null if not found

Initializes a new instance of the class. Constructor for serialization. Use FromSequenceRow to create new results for a raw file.

Initializes a new instance of the class.

The sequence row. The row.

Initializes a new instance of the class.

The sequence row. The row. The method. The keep signals. The adapter. The component progress. The integrator creator.

The integrate all components.

The file. The keep signals. The method. The component progress.

The integrate one component.

The file. The keep signals. The component progress. The mass options. The total components. The components completed. The component. The process retention time references. True on success.

Finds the results for component.

The name of the component to find. The results for the named component, or null if not found

Class to find results for a component.

Initializes a new instance of the class.

The dictionary.

Find results for a component.

The component name to find. The results for the named component. Null if the component is not found.

responses area added to the replicate tables for each component

The processing method used for calibration settings

Adds data from this file to calibration curves. If this file is a calibrator or QC, it is added to the replicates.

Processing method Replicate of calibration levels.

Calculate the amounts for all components in this file. Performs flagging on the amount.

Settings for all components (needed for flagging) Calibrated data for all components.

Calculate the amounts for all components in this file. Performs flagging on the amount, based on the components settings

Settings for all components (needed for flagging) Calibrated data for all components.

Make a results lookup table.

The lookup table

Creates a new object that is a copy of the current instance.

A new object that is a copy of this instance. 2

Copy all manually integrated peaks from previous results. This checks to see if the supplied results were from the same file. If there is no sample information, then the row number must match. If the samples match, then the results from matching components are preserved. This method supports re-integration from a changed method, preserving any manually integrated results from the previous integration.

previously integrated results

Class to perform flag evaluations for each sample type

Gets or sets a value indicating whether this is for an internal standard

Gets or sets the type of sample being analyzed

Gets or sets the sample dilution factor

Gets or sets the Limits to set the flags

Calculate flags for all sample types

Calibration statistics Area and Height of peak, plus ratios to ISTD Amount of standard or QC in this cal level Retention time of peak Calibration curve rSquared value Amount calculated for this compound The results of all tests.

Calcuate all flags.

The statistics access. The peak responses. The concentration. The retention time. The r squared. The standard amount. The results of all flag tests. The results of all tests.

Results of flag calculations per sample type

Gets or sets the results of the solvent blank tests

Gets or sets the results of the MatrixBlank tests

Gets or sets the results of the QC tests

Gets or sets the results of the calibration (standards) tests

Gets or sets the results of the quantitation (unknown sample) tests

Gets or sets the results of the internal standard tests

Initializes a new instance of the class. Create results, all set to "not tested"

Initializes a new instance of the class. Construct object from interface

To copy from

Creates a new object that is a copy of the current instance.

A new object that is a copy of this instance. 2

Thresholds for each sample type

Initializes a new instance of the class. Copy object

Object to copy

Initializes a new instance of the class. Default constructor

Initializes a new instance of the class.

The thresholds.

Gets or sets thresholds for unknowns (tests on Quantity)

Gets or sets thresholds on standards (quality of calibration curve)

Gets or sets thresholds on QCs

Gets or sets thresholds to flag Matrix blank samples

Gets or sets thresholds to flag internal standards

Gets or sets thresholds for Matrix Spike sample type

Gets or sets thresholds for Solvent Blank sample type

Creates a new object that is a copy of the current instance.

A new object that is a copy of this instance. 2

Build sample groups from a sequence

Create groups of samples out of the supplied sequence. Each group is a set of samples which should share a calibration curve.

Sequence to split A set of groups , identified by sequence row start (Item1) and end (Item2)

Create sub-sequences from a supplied sequence, based on a set of groups

The sequence to split The sub sequences.

Separate based on method

The sequence to separate The sub sequences

Extract a group. This removes any samples which are unique to this group from the list, and returns row numbers from the original sequence.

The range of samples in the group

Define a list of samples, which is a list of samples plus additional operations, allowing samples to be found by job number.

Initializes a new instance of the class.

Gets or sets the bracket tail.

remove the job with a given job number

The job number

find a job with a given job number return null if not found

The n job. The found job

Add to bracket.

The .

States of the bracket detection state machine.

The no brackets state.

The bracket start state.

The bracket qc state.

The bracket unknowns state.

The bracket end state.

Class for 1 sample in the list (equivalent to 1 sequence row)

Gets or sets the row index to the original sequence.

Gets or sets the job number

Gets or sets the job's sequence information.

Gets or sets the type of bracket this job belongs to.

Gets or sets a value indicating whether this job is shared between groups.

Gets or sets a value indicating whether this job was the last in its sequence file

Specify how an integrator is created from a component.

Component who's parameters can be used to select an integrator An integrator appropriate for this component

This class calculates quantitation results for a single component in a single raw file. This includes integration and all subsequent validation steps, such as Ion Ratio Confirmation and System Suitability.

Gets the quality control level for this component

Gets the calibration level for this component

Gets or sets the results of integrating this component

Gets the results of integrating this component

Gets the calibration level for this component

Gets the quality control level for this component

Initializes a new instance of the class. default constructor to support serialize

Initializes a new instance of the class. copy constructor

The access.

Begin the quantitation for a single component from one raw file. After all peaks are integrated, and a calibration curve has been calculated additional methods need to be called to get the final calculated amount. CalculateRatios should be called after all components in a file have been integrated. After all files have been processed, CalculateAmounts must be called to get the concentration.

The file whose data is integrated Method to find results for other components The component to integrate If true, the chromatogram signal and spectrum at peak apex are kept. This can save re-reading the signal to display chromatograms. tolerance to apply to mass chromatograms An integrated peak for this component. fileResults is null.

The file whose data is integrated Method to find results for other components The component to integrate If true, the chromatogram signal is kept. This can save re-reading the signal to display chromatograms. tolerance to apply to mass chromatograms Delegate which returns an integrator when supplied a component. Permits integrators not known to common core to be used. An integrated peak for this component. fileResults is null.

Make an integrator based on settings in a component

Component who's integration settings are used The created integrator.

A device has negative data?

The instrument type True if data may be negative

The find reference peak.

The component. The results finder. The reference peak, or new Peak() if not found.

Calculate the results.

The file. The component. The file results. The mass options. The ratio method. True if chromatogram signals should be kept. The integrated component results

The get scan information.

The file. The component. The store signal.

Method to get the results for a component. Applies to retention time references, internal standards etc.

Name of component to find

Calculate the response ratio for this component, using it's internal standard

The set of available components Delegate to find results for a given component

The calculate ratios using internal standard.

The target compound settings. The internal standard. The find component result.

Add this component to the calibration curve (replicate table), if it is standard. If this is a QC, add to a special QC replicate table, so that QC stats can be calculated. If there is no "PeakFound" then this has no action.

List of components Table of replicates (which will be updated) Parameters for this sample

Add a sample to the calibration curve

Component settings Fast lookup table for replicates by name Calibration level If true: add even if this is not a calibration sample sample information

Add a sample to the calibration curve

Component settings Replicates of this component Calibration level If true: add even if this is not a calibration sample sample information

This method determines if the sample is of a type which should be added to a calibration curve

Acquired sample type True if this is a calibrator

Copy the manual peaks from an equivalent component in prior results. Finds the results for the same component, and if it exists, copies the manual peak.

delegate to find matching data from previous results

The perform ion ratio checks.

The file. The component. The integrator. The mass options.

Add this sample to the calibration curve data. If this sample was not a calibration or QC level of the component, this has no effect. This locates the calibration or QC level for the sample in the replicate table for the component integrated. It then adds to the Calibration or QC replicates list, and records the calibration or QC level found. A key (typically file name) is saved in the component replicate table, so that it is easy to replace a replicate for a given file.

Replicates of standards for calibration The calibration or QC level for the current file Type of this sample If this is not set, then the level is searched in the calibration table, else in the QC table. Key saved with replicate to identify this sample

Calculate the amount for this component.

Settings for component (needed for flagging) Calibrated data for this component. Dilution of the sample, used in threshold calculations.

Calculate the amount for this component.

Settings for component (needed for flagging) Calibrated data for this component. sample information (cal level etc.).

The calculate sample flags.

The component access. The table. The sample.

The get replicate access.

The table. The is istd. The sample.

Copy a manually integrated peak from previous results

previously integrated results

Creates a new object that is a copy of the current instance.

A new object that is a copy of this instance. 2

All possible measurements of response from a peak

Gets the area of a peak

Gets the height of a peak

Gets the Response (which will be either CalculatedArea or CalculatedHeight, depending on method used)

Gets the ratio of CalculatedResponse to CalculatedResponse of ISTD. Same as CalculatedResponse for an ISTD, or when using external standards

Read only access to processing options

Gets if this is an internal or external standard method.

Gets the RSD calculation method.

The RSD calculation method.

provide read only access to a component

Gets the component name

Gets the chemical formula for the component

Gets a value which determines if this peak is a retention time reference, or used a reference

Gets a value indicating whether this component is being used for any kind of retention time reference

Gets chromatogram settings (use instead of ChroSettings, ChroSettings2 etc.).

Gets the smoothing data.

The smoothing data.

Gets the component to use for retention time adjustments

Gets a value indicating whether response flags are based on calculated amounts. Determines how response high and low is calculated. By default (false) the response high or low is set if the response of the component is outside of the calibration curve. This is: below the lowest standard or above the highest standard. If this flag is set to true, the flags are set based on the calculated amount being above or below the curve.

Gets the calibration settings.

The calibration settings.

Gets a value indicating whether a concentration can be calculated from this component.

Gets the width in minutes of "display" area, centered around the peak. Data used for processing can be restrained to this range, by setting UseBaselineWindow to false

Gets a value indicating whether the retention time is adjusted (by a reference)

Gets the precision (number decimals) to use for masses

Gets the system suitability (peak checks) for this component

Gets the ion ratio confirmation data.

The ion ratio confirmation data.

Gets the calibration and quantification data.

The calibration and quantification data.

Gets the detection threshold limits.

The detection threshold limits.

Gets the integration.

The integration.

Gets settings for PDA Peak purity calculation

Gets peak location settings, such as expected retention time

Gets Thresholds for evaluation of flags for various sample types

Provide read only access to a collection of components

Gets the set of components (target compounds and standards) in the method

Find a component in the method by name

The name to search for The found component, or null if no match

Provide read only access to a processing method

Gets the mass options.

The mass options.

Gets the processing options object. Don't need a setter function, always refer to the options from this method.

The processing options.

Access to results of the calibration and quantification flagging.

Gets a value indicating whether the sample is above the LOD.

Gets a value indicating whether [R square passed].

Gets a value indicating whether the value is below the limit of quantitation.

Gets a value indicating whether the sample is below the linearity limit.

Gets a value indicating whether the sample is below the carry over limit. This is usually displayed only for blanks.

Read only access to calculated results for a component

Gets the peak for use with manual mode

Gets a value indicating whether manual mode is selected, requesting "Peak" gets the manual peak

Gets the results of component detection. The detected peak plus additional data.

Gets a value indicating whether a peak has been found. Always true for manual peaks.

Gets a value indicating whether RT adjustments could be made. This flag is only meaningful when RT reference adjustments are made based on a reference peak (see the locate class). If a valid reference peak is supplied, then the expected RT can be adjusted based on the reference. If no reference peak is found (a null peak) then the expected RT cannot be adjusted, and this flag will be false.

Gets a reference back to component which created these results

Gets the scan at peak apex

The segmented scan object.

Gets a value indicating whether the data is centroid style This defines the data type (drawing style) of the Segmented Scan. If true: Plot as sticks (centroid data) else plot as connected lines (profile data)

Gets the scan stats.

The scan stats.

Gets the chromatogram trace for this peak

Gets data such as serial number for the instrument used to read the chromatograms. This can be null when there is no valid data. (no signal read yet).

Gets the ratio of height to internal standard height

Gets the ratio of area to internal standard area

Gets a value which determines how ratios are reported, either by height or area. This is initialized from the component in "FromComponent"

Gets the internal standard area

Gets the internal standard height

Gets the amount calculated for this component

Gets information about the peak relative to the calibration curve, such as "Response High"

Gets the results of system suitability checks

Gets the results of all IRC calculations for this component

Gets a value indicating whether all IRC tests have passed, or IRC is never run.

Gets the calibration and quantification flags.

The calibration and quantification flags.

Gets the detection threshold flags.

The detection threshold flags.

Gets the ion ratio signals.

The ion ratio signals.

Gets the value to use for the calibration curve. Either the area ratio or height ratio (depending on calibration settings)

Gets either the or depending on the methodCalibrationSettings. TargetCompoundSettings.Response.

The method calibration settings. The response for this component

Gets results of flag calculations per sample type

Read only access to Thresholds for each sample type

Gets thresholds for unknowns (tests on Quantity)

Gets thresholds on standards (quality of calibration curve)

Gets thresholds on Quality control samples

Gets thresholds to flag Matrix blank samples

Gets Thresholds to flag internal standards

Gets Thresholds for Matrix Spike sample type

Gets Thresholds for Solvent Blank sample type

Read only access to one Quantitative sample

Gets the full name and path of the raw file, including the file extension.

Gets a value indicating whether this row is a startup method row

Gets a value indicating whether this row is a shutdown method row This item will not appear in a raw file, but can appear on sample submission.

Gets the revision number of this sample row

Gets the GUID for application tracking of this data

Gets the comment about sample (from user).

Gets the Code to identify sample.

Gets the description of sample.

Gets the vial or well form auto sampler.

Gets the amount of sample injected.

Gets bar code from scanner (if attached).

Gets the bar code status.

Gets a Name to identify the Calibration or QC level associated with this sample. Empty if this sample does not contain any calibration compound.

Gets the bulk dilution factor (volume correction) of this sequence row.

Gets the instrument method filename of this sequence row.

Gets the name of acquired file (excluding path).

Gets the name of calibration file.

Gets the ISTD amount of this sequence row.

Gets the row number.

Gets the path to original data.

Gets the processing method filename of this sequence row.

Gets the type of the sample.

Gets the sample volume of this sequence row.

Gets the sample weight of this sequence row.

Gets the collection of user text.

Read only access to replicate table for one component

Gets the name of component which made this replicate table

Gets the fitted regression from this table.

Create the sets of points needed to display a calibration curve.

The calibration curve points

Gets the settings used to create this table

Gets the amount of the lowest calibration level (low limit of calibration)

Gets the amount of the highest calibration level (high limit of calibration)

Gets the highest response included on the calibration curve. This is only valid after the curve has been created.

Gets the lowest response included on the calibration curve. This is only valid after the curve has been created.

Finds the replicate with amount and response from the current sequence replicates table.

The amount. The response. null if not found.

Finds the replicate with amount and response from the historic sequence replicates table.

The amount. The response. null if not found.

Finds the replicate with amount and response from the the current sequence or the historic sequence replicates table. The current sequence data is searched first.

The amount. The response. null if not found.

Finds the item with the name that matches the level.

The level. Replicates for the level, or null if not found

Finds the item with the name that matches the level.

The level to find Replicates for the level, or null if not found

Finds the item with the name that matches the level, in the historic replicates table.

The level.

Read only access to quantitation results for a single component in a single raw file. This includes results of integration and all subsequent validation steps, such as Ion Ratio Confirmation and System Suitability.

Gets the quality control level for this component

Gets the calibration level for this component

Gets the results of integrating this component

read only access to integration for all components in 1 file.

Gets the sample information for this raw file

Gets the zero based index into the sequence for this row

Gets the summary information about the rawfile

Finds the results for component.

The name of the component to find. The results for the named component, or null if not found

Methods to update the integration results of a file, after recalibration etc.

responses area added to the replicate tables for each component

The processing method used for calibration settings

Adds data from this file to calibration curves. If this file is a calibrator or QC, it is added to the replicates.

Processing method Replicate of calibration levels.

previously integrated results

Calculate the amounts for all components in this file. Performs flagging on the amount.

Settings for all components (needed for flagging) Calibrated data for all components.

Aggregate interface to read or modify results

Results of flag calculations per sample type

Gets the results of the quantitation (unknown sample) tests

Gets the results of the calibration (standards) tests

Gets the results of the QC tests

Gets the results of the MatrixBlank tests

Gets the results of the internal standard tests

Gets the results of the solvent blank tests

Interface to perform flag evaluations for each sample type

Gets or sets a value indicating whether this is for an internal standard

Gets or sets the type of sample being analyzed

Gets or sets the sample dilution factor

Gets or sets the Limits to set the flags

Calculate flags for all sample types

Defines a sequence of quantitative samples

Gets the Name of the sequence

Gets a value which defines how calibration sets are bracketed

Gets All samples in this sequence

Gets Headings for user defined sequence columns

Defines a sequence of quantitative samples

Gets or sets the name of sequence

Gets or sets a value which defines how calibration sets are bracketed

Gets or sets all samples in this sequence

Gets or sets headings for user defined sequence columns

Class to perform flag evaluations on internal standards

Gets or sets limits for internal standard

perform flag evaluations on internal standards

Average of internal standard areas Area of the internal standard Average retention time of internal standards retention time of this peak Calculated % CV from the replicate table Calculated flags for internal standard

Get the coefficient of variance status.

The coefficient of variance. Pass, Fail or Not Tested result for CV.

Get the retention time in range status.

The retention time. The average retention time. Pass, Fail or Not Tested result for RT.

Get the area in range status.

The area. The average area. Pass, Fail or Not Tested result for area.

Results of Internal Standard flag Testing

Gets or sets the results of testing the area is within limits

Gets or sets the results of testing the retention time is within limits

Gets or sets the results of testing the CV is blow limits

Initializes a new instance of the class. Default constructor: all results not tested yet

Initializes a new instance of the class. copy object

object to copy

Creates a new object that is a copy of the current instance.

A new object that is a copy of this instance. 2

Criteria for evaluation of Internal Standards

Initializes a new instance of the class. Create a copy of this object from an interface

Object to copy from

Initializes a new instance of the class. Default constructor

Gets or sets the maximum acceptable coefficient of variation for ISTD compounds

Gets or sets the minimum acceptable recovery of the ISTD (from sample prep).

Gets or sets the maximum acceptable recovery of the ISTD (from sample prep).

Gets or sets the maximum value of Retention Time, deviation below average, acceptable

Gets or sets the maximum value of Retention time, deviation above average, acceptable

Creates a new object that is a copy of the current instance.

A new object that is a copy of this instance. 2

This class holds all replicates of a single component

Add a replicate to the collection. This will replace a replicate with the same level and key.

Add a replicate of this calibration level Response of the replicate peak Retention time of peak Key to save with this replicate (for example, filename) The calibration level

Add a replicate to the collection. This will replace a replicate with the same level and key.

Add a replicate of this calibration level Response of the replicate peak Key to save with this replicate (for example, filename) The calibration level

Add a replicate to the collection. This will replace any replicate with the same level, key and peakKey

Add a replicate of this calibration level Response of the replicate peak Primary key to save with this replicate (for example, filename) Second key for this data, for example peak name (compound, component or analyte) The calibration level

Add a replicate to the collection. This will replace any replicate with the same level, key and peakKey

Add a replicate of this calibration level Response of the replicate peak Retention time of peak Primary key to save with this replicate (for example, filename) Second key for this data, for example peak name (compound, component or analyte) The calibration level

Find a replicate table for a calibration level which has a given amount

The amount to find the found level, or null

Find a replicate table matching a supplied level name

Level to search for The found replicate table or null if nothing matches

Copy any exclusions for matching replicates in a previous replicate table, for example, when the table is recreated after reintegrating one peak or manual integration.

Where the exclusions are copied from

Find a table of replicates matching a calibration level

Calibration level to look for A table for the selected calibration level

Test if levels are the same.

The first. The second. True if levels are the same.

Create a table of points to draw on a calibration curve

if true, create points for the included data, else create points for the excluded data The list of points to plot

Calculate flags for MatrixBlank sample type

Gets or sets the flagging thresholds on quantity

Gets or sets the rules for matrix blank testing

Calculate flags for MatrixBlank sample type

The calculated amount Test results

Convert to status from test result.

The threshold. The test result. The .

Get carryover status.

The calculated amount. The factor. The . Thrown if the matrix blank method is invalid.

Get carryover status max concentration.

The calculated amount. The .

Get carryover status Limit Of Quantitation.

The calculated amount. The factor. The .

Get carryover status Limit Of Detection.

The calculated amount. The factor. The .

Get carryover status Limit Of Reporting.

The calculated amount. The factor. The .

Results of Matric Blank flag Testing

Gets or sets the status of the "carryover" test, by the specified method and threshold

Initializes a new instance of the class. Default constructor, no flag tested

Initializes a new instance of the class. Create a copy

object to copy

Creates a new object that is a copy of the current instance.

A new object that is a copy of this instance. 2

Thresholds for flagging a Matrix Blank sample

Gets or sets a value which determines what criteria is used to evaluate a matrix blank sample

Initializes a new instance of the class. Create a copy of this object from an interface

Object to copy from

Initializes a new instance of the class.

Gets or sets the percentage. The test is performed at this percent of the thresholds specified in "Method". For example, to flag is the carryover in the blank is 2% of LOR, set Method to LimitOfReporting and Percentage to 2. If the method is "MaxConcentration" then the value of the MaxConcentration property is used (not a percentage)

Gets or sets the maximum concentration of compound in MatrixBlank. Used only when method is "MaxConcentration"

Creates a new object that is a copy of the current instance.

A new object that is a copy of this instance. 2

Calculate flags for matric spike sample type

Perform flag evaluation

Limits for matrix spike testing The .

Results of Matrix spike tests

Gets or sets the results of the Spike Recovery test

Gets or sets the results of the Recovery Percent Difference test

Creates a new object that is a copy of the current instance.

A new object that is a copy of this instance. 2

Limits for testing matrix spike samples

Initializes a new instance of the class. Create a copy of this object from an interface

Object to copy from

Initializes a new instance of the class. Default constructor

Gets or sets concentration of sample spiked into matrix

Gets or sets the calculated concentration of the sample, expressed as a percentage of theoretical concentration, should be above the min recovery %

Gets or sets the calculated concentration of the sample, expressed as a percentage of theoretical concentration, should be below the max recovery %

Gets or sets the maximum relative percent difference between 2 spiked samples

Creates a new object that is a copy of the current instance.

A new object that is a copy of this instance. 2

Defines replicates for all components in a method

Gets the replicate tables (one per component).

Initializes a new instance of the class.

Initializes replicates based on the supplied method.

Initializes a new instance of the class.

Initialize the replicates.

The processing method.

Get a copy of the replicates.

The copy

The find matching replicate table.

The component replicate table. The .

Create calibration curves.

(Optional) historic Replicates. If this is not null or empty, and has replicates for these components, then include them in the curves.

Get a read only collection of these tables

The tables

copy replicates from another object.

The replicate tables to copy.

A method for quantitative processing. The method contains a list of components, to be detected and quantitated.

Gets or sets the mass options.

The mass options.

Gets or sets the processing options object. Don't need a setter function, always refer to the options from this method.

The processing options.

Gets the set of components (target compounds and standards) in the method

Initializes a new instance of the class. Default Constructor

Initializes a new instance of the class. Construct instance from interface, by cloning all settings

Interface to clone

Gets the mass options.

Gets the processing options object. Don't need a setter function, always refer to the options from this method.

The processing options.

Gets the set of components (target compounds and standards) in the method

Find a component in the method by name

The name to search for The found component, or null if no match

Gets the processing options object. Don't need a setter function, always refer to the options from this method.

The processing options.

Find a component in the method by name

The name to search for The found component, or null if no match

Implementation of ICloneable.Clone method. Creates deep copy of this instance.

An exact copy of the current object.

Copies to the copy method.

Object to copy into copy is null.

Updates the component list.

Adds a new component with the name before the .

The new name. Name of the selected. if set to true, [after new name]. The default component to clone the new component to. If this is null, then set the new component to a clone of the selected component and change the name. An enumeration which details if the operation worked, or how it failed. ArgumentException(NullComponet): if cannot be found in components list. ArgumentOutOfRangeException: if not index of is out of range (serious programming error).

Renames the component which has "oldName" to be called "newName".

The new name. The old name. An enumeration which details if the rename worked, or how it failed.

Deletes the component named.

Name of the component to delete. A value which determines if the operation succeeded, or the reason for failure.

Initializes a new instance of the class.

The method. Optional mass options. This may be null. If not null, the supplied options override those saved in the method. For example: when requesting a filter string

Provides a delegate to open files for specific extensions given the 'type' and 'assembly'. The class calls the method that has a single string parameter and returns an ''. This class can also be used in conjunction with the ''. In such a situation, it is not required that Initialize' is called.

Initializes a new instance of the class. Associates the extension, class type and the assembly with this instance. The method name can also be passed if it is different. However, for the method to be invoked it needs to match the delegate's signature.

file extension fully qualified class name to initialize fully qualified assembly name method name (defaults to "FileFactory")

Initializes a new instance of the class.

The method to open a processing method file, given a file name. The extension.

Represents the strongly typed collection of objects that can be Individually accessed by index.

Initializes a new instance of the class. Create a collection of Processing Method creators, adding default objects to the collection. This can open pmd or XML format files.

Class to read processing methods from a file

Create method from xml (file)

The file name. The .

Create method from PMD (file)

The file name. The .

Create method from PMD file overriding mass precision

The file name. Mass options, used when formatting scan filter text The .

Contains the options for this processing method

Initializes a new instance of the class. Default constructor

Initializes a new instance of the class. Construct instance from interface, by cloning all settings

Interface to clone

Initializes a new instance of the class.

The access.

Gets or sets the calibrate by.

The calibrate by.

Gets or sets the RSD calculation method.

The RSD calculation method.

Implementation of ICloneable.Clone method. Creates deep copy of this instance.

An exact copy of the current object.

Calculate flags on Qc sample type

Calculate flags on Qc samples

Limits to test stats for this QC level The response ratio for this sample Flag results after testing QC sample

The get response factor within limits status.

The thresholds. The average response factor. The response factor. The .

The get cv test status.

The thresholds. The percent cv. The .

Results of Qc flag Testing

Gets or sets results of testing the curve "RSquared" value against the minimum. Must be above minimum for this to pass

Gets or sets result of testing that %CV is in bounds

Initializes a new instance of the class. Default constructor. Sets all results to not tested.

Initializes a new instance of the class. Make a copy

object to copy

Creates a new object that is a copy of the current instance.

A new object that is a copy of this instance. 2

Thresholds on QC samples

Gets or sets maximum percent difference from the relative response (response factor) of this sample, to the average

Gets or sets maximum value of percent CV

Initializes a new instance of the class. Create a copy of this object from an interface

Object to copy from

Initializes a new instance of the class. Default constructor

Creates a new object that is a copy of the current instance.

A new object that is a copy of this instance. 2

Component definition for quantitation (target compound)

Gets or sets the component name

Gets or sets the chemical formula for the component

Gets or sets a value which determines if this peak is a retention time reference, or used a reference

Gets a value indicating whether this component is being used for any kind of retention time reference

Gets the smoothing parameters.

Gets or sets chromatogram settings (use instead of ChroSettings, ChroSettings2 etc.).

Gets or sets the smoothing data.

The smoothing data.

Gets or sets the name of the component to use for retention time adjustments

Gets or sets a value indicating whether response tests are based on the calculated amount. Determines how response high and low is calculated. By default (false) the response high or low is set if the response of the component is outside of the calibration curve. This is: below the lowest standard or above the highest standard. If this flag is set to true, the flags are set based on the calculated amount being above or below the curve.

Gets the calibration settings.

The calibration settings.

Gets the calibration settings.

The calibration settings.

Gets or sets the calibration settings.

The calibration settings.

Gets a value indicating whether a concentration can be calculated from this component.

Gets or sets the width in minutes of "display" area, centered around the peak. Data used for processing can be restrained to this range, by setting UseBaselineWindow to false

Gets a value indicating whether the retention time is adjusted (by a reference)

Gets or sets the precision (number decimals) to use for masses

Gets or sets the system suitability (peak checks) for this component

Gets or sets the ion ratio confirmation data.

The ion ratio confirmation data.

Gets or sets the calibration and quantification data.

The calibration and quantification data.

Gets or sets the detection threshold limits.

The detection threshold limits.

Gets or sets the integration.

The integration.

Gets or sets settings for PDA Peak purity calculation

Gets or sets peak location settings, such as expected retention time

Gets or sets thresholds for evaluation of flags for various sample types

Gets the Thresholds for evaluation of flags for various sample types

The calibration settings.

Gets chromatogram settings (use instead of ChroSettings, ChroSettings2 etc.).

Gets the peak location settings, such as expected retention time

Gets settings for PDA Peak purity calculation

Gets the integration settings.

The integration.

Gets the detection threshold limits.

The detection threshold limits.

Gets the ion ratio confirmation data.

The ion ratio confirmation data.

Gets the calibration and quantification data.

The calibration and quantification data.

Gets the system suitability (peak checks) for this component

Initializes a new instance of the class. Default constructor

Initializes a new instance of the class. Constructor, which should be used when not serializing, with the parameter set "true"

When true: default events are added to the Avalon integrator. This is not needed when the object is about to be used by a serializer, as in that case the initial settings will already be in the serialized object

The create component.

The initialize.

Initializes a new instance of the class. Construct instance from interface, by cloning all settings

Interface to clone

Initializes a new instance of the class.

The access. The options.

Copies to the input component, line by line.

The component.

Implementation of ICloneable.Clone method. Creates deep copy of this instance.

An exact copy of the current object.

Copies the non-primitive objects.

The component.

Calculate flags for "unknowns"

Gets or sets thresholds to test against

Apply the dilution factor to the quantity before flag testing

Amount with no dilution Dilution to apply Diluted quantity

Evaluate flags for unknowns

Amount of unknown Results of quantity flagging

Convert a bool to a result status

result of flagging test Status (pass if result is true)

Test if the calculatedAmount is at or above a threshold.

Thresholds to test against Quantity calculated If the threshold is set to zero, the result is "Not Tested". The result is "pass" when greater or equal to a non zero threshold, else fail

Test if a value is within a limit (less than or equal to the limit), or not tested, when the limit is zero

Amount to test Threshold to test (or zero) Status of test

The get carryover status.

The calculated amount. The .

The get limit of detection status.

The calculated amount. The .

The get limit of linearity status.

The calculated amount. The .

The get limit of quantitation status.

The calculated amount. The .

The get limit of reporting status.

The calculated amount. The .

Defines one sample in the common core Quantitation model

Gets or sets a value indicating whether this row is a startup method row

Gets or sets a value indicating whether this row is a shutdown method row This item will not appear in a raw file, but can appear on sample submission.

Gets or sets revision number of this sample row

Gets or sets GUID for application tracking of this data

Initializes a new instance of the class. One sample (one raw file) in a sequence to quantitate

Initializes a new instance of the class. copy a sample

The access.

Initializes a new instance of the class.

The access.

Gets the full name and path of the raw file, including the file extension.

Results of tests on quantity

Gets or sets results of the Limit of detection test. This is "Passed" if the calculated amount is equal to or above the limit of detection

Gets or sets results of the limit of quantitation test This is "Passed" if the calculated amount is equal to or above the limit of quantitation

Gets or sets results of the limit of reporting test. This is "Passed" if the calculated amount is equal to or above the limit of reporting

Gets or sets results of the limit of linearity test. This is "Passed" if the calculated amount is equal to or below the limit of Linearity

Gets or sets results of the carryover test. This is "Passed" if the calculated amount is equal to or below the carryover limit

Gets a Flag for sample "failed" if it is between these limits. If either of LimitOfQuantitationStatus or LimitOfDetectionStatus are NotTested, then this is NotTested If the sample passed (above) the LOD test, but failed (below) the LOQ test then this returns "Fail", else "Pass"

Initializes a new instance of the class. Default constructor. All results are set to "not tested"

Initializes a new instance of the class. Make a copy of this object

Object to copy

Creates a new object that is a copy of the current instance.

A new object that is a copy of this instance. 2

Thresholds on Quantity (for unknowns)

Initializes a new instance of the class. Create a copy of this object from an interface

Data to copy

Initializes a new instance of the class. Default constructor

Initializes a new instance of the class.

The thresholds. if thresholds is null

Gets or sets the Lowest detectable quantity

Gets or sets the smallest acceptable quantity

Gets or sets the Smallest quantity which should be reported

Gets or sets the Maximum quantity which has a "linear" response. If this is set to "zero" then all responses are considered good.

Gets or sets the Maximum quantity which would not cause carryover. If this is set to "zero" then all responses are considered good.

Creates a new object that is a copy of the current instance.

A new object that is a copy of this instance. 2

Class to hold summary data about a raw file, which may be needed for a report

Gets or sets the name of person acquiring the data

Gets or sets the number of scans acquired

Gets or sets the lowest mass in file (for MS data)

Gets or sets the highest mass in file (for MS data)

Gets or sets the path where raw data was originally acquired

Gets or sets the acquisition duration (minutes):

Gets or sets the time stamp for raw data

Creates a new object that is a copy of the current instance.

A new object that is a copy of this instance. 2

Initialize a raw file information object from a raw file

File to read from File summary information

Method which calculates a statistic from an array of doubles.

Array to analyze Results of statistical calculation

Class to add CV and Percent RSD results to replicates

Gets or sets Coefficient of variance of responses for standards and QCs.

Gets or sets Average value of the response factor

Gets a value indicating whether the replicate is valid. Implementation from IReplicateStatisticsAccess This will be true for all replicates with an assigned level name

Gets or sets RSD on calculated amounts of standards and QCs

Gets or sets Average value of retention time for all peaks added

Initializes a new instance of the class.

The level.

Initializes a new instance of the class. Default constructor

Calculate stats for level.

The regression. The percent RSD calculator.

Apply any exclusions in a prior set of replicates to these replicates.

Replicates to copy from.

A collection of samples. Based on Xcalibur Home Page and LCQuan. Supports relative paths to method files.

Gets or sets all samples in this sequence

Gets or sets a value which defines how calibration sets are bracketed

Gets or sets headings for user defined sequence columns

Gets or sets the name of the sequence

Gets read only access to all samples in this sequence

Initializes a new instance of the class. Default constructor

Initializes a new instance of the class. Copy constructor

The access.

Initializes a new instance of the class. Construct from a list of samples

samples to add

Initializes a new instance of the class. Construct from a list of samples, bracket type and user labels

Samples to add Type of bracketing used Labels for user sequence columns

Initializes a new instance of the class.

The file. Thrown for null file name

This method looks for paths which begin with "$" and replaces "$" with the supplied "rootPath". Calling "validate paths" after this will validate that all methods and raw files exist in the supplied paths.

The root Path.

Test that every instrument method, processing method and data file exists. If the "processing method", "Instrument method" or "file" is an empty string, then this file is skipped, and does not cause a "false" return. When "raw file name" is tested, the system will check first if the file exists "as is". It will then test the path+file name + each supplied extension. Extensions must include the "." (such as ".raw"). If the file is found with at least one extension, then this is considered valid.

The data File Extensions. true if each "non empty" file name in the sequence points to an existing file.

Create xml processing method name.

The method name base. The .

Creates a new sequence object out of an existing sequence, with the rows corresponding to a bracket.

The range of samples to extract The .

Make a copy of this object

A copy of this object

Provides a delegate to open sequence files for specific extensions given the 'type' and 'assembly'. The class calls the method that has a single string parameter and returns an ''. This class can also be used in conjunction with the ''. In such a situation, it is not required that Initialize' is called.

file extension fully qualified class name to initialize fully qualified assembly name method name to call (defaults to "FileFactory")

Initializes a new instance of the class.

The method to open a sample sequence file, given a file name. The extension.

Represents the strongly typed collection of objects that can be Individually accessed by index.

Initializes a new instance of the class. Create a collection of Processing Method creators, adding default objects to the collection. This can read Xcalibur sld files and XML formatted sequences.

Factory class to read a sample sequence, from XML.

Create sequence from xml.

The file name. The .

Create sequence from xml.

The file name. The .

The integration results for all files in a sequence.

Get keys for all samples.

The collection of keys

The results for a specific sample

identifier for sample The .

Add all results to calibration curves.

The method access. The replicate tables.

Recalculate the amounts for all samples

The method. The replicate tables.

Copy a manually integrated peak from previous Sequence Integration Results

previously integrated results

Copy a manually integrated peak from previous results

method to return previously integrated results for a sample

Copy results from another object

The other object

The emulation mode for peak integration.

original common core, as of approximatly 2012. This behaviour was " as used by trace finder" before a more extensive anaysis found that the code at that time was not an exact copy of the Xcalibur algorithms.

emulate Quan Browser This will contine to correct for any defects filed, from stanard Xcalibur results, especially deviations from Quan Browser, inclusing any deviatiosn from qualitatave processing as found in "qualitative proicessing setup" or "qual browser". Such issues are found by replacement applications for legacy Xcalibur code, such as Freestyle project.

emulate LcQuan This is same as emulation of Quan Browser, except where processing is found to be different in the packages LCQuan. This case is added, as LCquan has it's own souce code for quan algorithms, which may have diverged from Xcalibur.

Class to perform integration of all files in a sequence. Supports parallel file processing.

Initializes a new instance of the class. Default constructor.

Gets or sets the application emulation mode.

Gets or sets the maximum number of active threads. That is: the max number of open raw files. Defaults to the "number of available processors".

Gets or sets a value indicating whether parallel code can be used. This permits many raw files to be processed in parallel.

Make an integrator based on settings in a component

Component who's integration settings are used The created integrator.

Open a processing sequence.

The sequence. The processing method The file factory. The .

A device has negative data?

The instrument type True if data may be negative

process one work item.

The work item.

Add work to the work list. If there are insufficient background workers, assign more.

Collection of work New job to add

add a worker.

The work.

Generate the chromatogram chunks, for all work items that this thread sees.

The work items.

Class to perform integration of one file (in a thread)

Initializes a new instance of the class. Save the work to be done (does not do any calculations)

The sequence row The sample information (cal level etc.) The processing method A delegate which returns raw data A delegate which returns a peak integrator

Gets the Results of integrating one file

Process the raw data

The sequence quantitation results. This includes: The integration results for all samples ina sequence. The calibration curve information (replicate table) for all components.

Initializes a new instance of the class.

The processing method, needed to initialize the replicates.

Initializes a new instance of the class.

Gets the integration results, for all files in the sequence.

copy results from another object

The other.

Gets the calibration replicate table, for all components in the method.

Apply exclusions (to calibration points), based on exclusions in a prior table. This is useful for recalibrating: An application can: 1: Cache the current replicates. 2: Regenerate the replicates from new integrations. 3: Use the cached replicates to maintain any exclusions set.

The prior replicates.

Calibrate. Builds calibration curves, and calculates all amounts.

The method.

Modify the results based on a change (for example, a peak has been modified by manual baseline) This does not re-integrate any data. Calibration curves are regenerated, and calculated amounts etc. recalculated.

The processing method used to generate the results.

Add a new sample to the results. This must be results from the next sample in a sequence of samples.

Method used for processing this sample Results for one sample

Replace one sample in the results. This works as follows: The integration results list is updated, such that the file with the same sample GUID as the supplied results is replaced by the new results. The order of the list is unchanged

Method used for processing this sample Results for one sample true if the result was found and updated

Set the table of replicates which came from prior sequences. The calibration curve is updated with the new replicates, and all amounts are recalculated. All subsequent calibration calculations with this object will continue to have these replicates included. To stop including the historic replicates, call

Processing method, with flagging settings etc. which are used to recalibrate the results Replicates from previous sequence

Stop using the historic replicates, as set by . Calibration curves are recalculated, based on current sequence replicates only, and all amounts are recalculated.

Processing method used for recalibration

Class to calculate flags for solvent blank sample type

Gets or sets thresholds for solvent blank testing.

Calculate flags for solvent blank sample type

response for this component. Calculated flags

Calculate response status.

The response. The .

Results of tests on Solvent blank samples

Gets or sets a flag for response being within limits

Initializes a new instance of the class. Copy object

object to copy

Initializes a new instance of the class. Default constructor: all flags are not tested

Creates a new object that is a copy of the current instance.

A new object that is a copy of this instance. 2

Limits for flag testing on Solvent Blank sample type

Initializes a new instance of the class. Copy object

Object to copy

Initializes a new instance of the class. Default constructor

Gets or sets the maximum response permitted in a solvent blank

Creates a new object that is a copy of the current instance.

A new object that is a copy of this instance. 2